class jade.basic.structure.SQLPose.PDB_database(database)

This class is specifically for if we already have a database. Note: This is not a ROSETTA database. If you need to convert this, use ROSETTA (Which now works in PyRosetta!) Functions are to output the database as a PDB, output specific pieces of protein as a pdb and query the database.

query_all(table='pdb')

query_chain(table, chain)

query_modelID(table, modelID)

query_pdbID(table, pdbID)

query_pdbID_and_chain(table, pdbID, chain)

query_pdbID_and_strucID(table, pdbID, strucID)

query_piece(table, start, end, chain)

query_piece_pdbID(table, pdbID, start, end, chain)

query_piece_pdbID_and_strucID(table, pdbID, start, end, chain, strucID)

query_strucID(table, strucID)

save_cur_as_pdb(outpath, supress_modelSep=False)

Saves the DB at the current cursor to a file. Make sure cursor is on the pdb table.

save_whole_db_as_db(filename, seperate_structures=False)

Saves the whole database in MEMORY to a file….

scrub(table_name)

This should help protect from sql injection. Not that it’s important now, but… Author:OrangeOctopus from stack overflow

set_output_DIR(outDIR)

set_output_occupancy_1(bool)

Output structures with 1.0 as occupancy. Mainly for Rosetta use.

update_modelID_CDRS(table)

Updates modelID to specify L1 through H3 and framework for possible future statistical analysis.

class jade.basic.structure.SQLPose.SQLPose(pdbID, modelID, structID, memory=False, path='')

fetch_and_read_pdb_into_database(pdbID, read_header=False, header_only=False)

Uses the PDB file specified, grabs it from the PDB, and reads the data in.

read_pdb_into_database_flat(filePath, specific_chain=False, read_header=False, header_only=False)

Reads the flat filepath specified into a database structure. This can then be parsed using the PDB_Database class. NOTE: Reading of header not implemented. if header_only is True, only loads the header. Useful for just getting specific information. More useful to D/L it from the pdb if possible. If Header only, reads the header into the database.

set_basic_options(pdbID, modelID, structID)

set_modelID(modelID)

set_pdbID(pdbID)

set_structID(structID)